[2024-01-25 20:08:05,670] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:08:05,672] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:08:05,672] [INFO] DQC Reference Directory: /var/lib/cwl/stg0d146ae9-4dfb-4d69-a2b5-28a658f28d31/dqc_reference
[2024-01-25 20:08:06,859] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:08:06,860] [INFO] Task started: Prodigal
[2024-01-25 20:08:06,860] [INFO] Running command: gunzip -c /var/lib/cwl/stg7a9f6ffb-da21-49ef-a12a-bd13fc7ed5fe/GCF_001997185.1_ASM199718v1_genomic.fna.gz | prodigal -d GCF_001997185.1_ASM199718v1_genomic.fna/cds.fna -a GCF_001997185.1_ASM199718v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:08:20,712] [INFO] Task succeeded: Prodigal
[2024-01-25 20:08:20,713] [INFO] Task started: HMMsearch
[2024-01-25 20:08:20,713] [INFO] Running command: hmmsearch --tblout GCF_001997185.1_ASM199718v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0d146ae9-4dfb-4d69-a2b5-28a658f28d31/dqc_reference/reference_markers.hmm GCF_001997185.1_ASM199718v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:08:20,950] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:08:20,951] [INFO] Found 6/6 markers.
[2024-01-25 20:08:20,992] [INFO] Query marker FASTA was written to GCF_001997185.1_ASM199718v1_genomic.fna/markers.fasta
[2024-01-25 20:08:20,992] [INFO] Task started: Blastn
[2024-01-25 20:08:20,992] [INFO] Running command: blastn -query GCF_001997185.1_ASM199718v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d146ae9-4dfb-4d69-a2b5-28a658f28d31/dqc_reference/reference_markers.fasta -out GCF_001997185.1_ASM199718v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:08:21,977] [INFO] Task succeeded: Blastn
[2024-01-25 20:08:21,980] [INFO] Selected 12 target genomes.
[2024-01-25 20:08:21,980] [INFO] Target genome list was writen to GCF_001997185.1_ASM199718v1_genomic.fna/target_genomes.txt
[2024-01-25 20:08:21,986] [INFO] Task started: fastANI
[2024-01-25 20:08:21,986] [INFO] Running command: fastANI --query /var/lib/cwl/stg7a9f6ffb-da21-49ef-a12a-bd13fc7ed5fe/GCF_001997185.1_ASM199718v1_genomic.fna.gz --refList GCF_001997185.1_ASM199718v1_genomic.fna/target_genomes.txt --output GCF_001997185.1_ASM199718v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:08:35,480] [INFO] Task succeeded: fastANI
[2024-01-25 20:08:35,481] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0d146ae9-4dfb-4d69-a2b5-28a658f28d31/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:08:35,481] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0d146ae9-4dfb-4d69-a2b5-28a658f28d31/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:08:35,489] [INFO] Found 12 fastANI hits (4 hits with ANI > threshold)
[2024-01-25 20:08:35,490] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:08:35,490] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Stenotrophomonas maltophilia	strain=ATCC 13637	GCA_001997185.1	40324	40324	type	True	100.0	1575	1579	95	conclusive
Stenotrophomonas maltophilia	strain=NCTC10257	GCA_900186865.1	40324	40324	type	True	99.9931	1578	1579	95	conclusive
Stenotrophomonas maltophilia	strain=NBRC 14161	GCA_001591205.1	40324	40324	type	True	99.9529	1516	1579	95	conclusive
Stenotrophomonas maltophilia	strain=MTCC 434	GCA_000597745.1	40324	40324	type	True	99.9218	1450	1579	95	conclusive
Stenotrophomonas sepilia	strain=SM16975	GCA_003244875.1	2860290	2860290	type	True	91.9044	1246	1579	95	below_threshold
Stenotrophomonas pavanii	strain=DSM 25135	GCA_001431565.1	487698	487698	type	True	91.7342	1198	1579	95	below_threshold
Stenotrophomonas pavanii	strain=LMG 25348	GCA_900101175.1	487698	487698	type	True	91.716	1259	1579	95	below_threshold
Stenotrophomonas pennii	strain=Sa5BUN4	GCA_014836545.1	2762239	2762239	type	True	84.5193	881	1579	95	below_threshold
Stenotrophomonas acidaminiphila	strain=DSM 13117	GCA_024221815.1	128780	128780	type	True	83.5993	809	1579	95	below_threshold
Stenotrophomonas pictorum	strain=JCM 9942	GCA_001310775.1	86184	86184	type	True	83.0688	505	1579	95	below_threshold
Xanthomonas indica	strain=PPL560	GCA_022669045.1	2912242	2912242	type	True	82.5068	827	1579	95	below_threshold
Xanthomonas translucens	strain=ATCC 19319	GCA_020880735.1	343	343	type	True	82.3659	660	1579	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:08:35,491] [INFO] DFAST Taxonomy check result was written to GCF_001997185.1_ASM199718v1_genomic.fna/tc_result.tsv
[2024-01-25 20:08:35,492] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:08:35,492] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:08:35,492] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0d146ae9-4dfb-4d69-a2b5-28a658f28d31/dqc_reference/checkm_data
[2024-01-25 20:08:35,493] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:08:35,541] [INFO] Task started: CheckM
[2024-01-25 20:08:35,541] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001997185.1_ASM199718v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001997185.1_ASM199718v1_genomic.fna/checkm_input GCF_001997185.1_ASM199718v1_genomic.fna/checkm_result
[2024-01-25 20:09:32,460] [INFO] Task succeeded: CheckM
[2024-01-25 20:09:32,462] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:09:32,485] [INFO] ===== Completeness check finished =====
[2024-01-25 20:09:32,485] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:09:32,486] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001997185.1_ASM199718v1_genomic.fna/markers.fasta)
[2024-01-25 20:09:32,486] [INFO] Task started: Blastn
[2024-01-25 20:09:32,486] [INFO] Running command: blastn -query GCF_001997185.1_ASM199718v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d146ae9-4dfb-4d69-a2b5-28a658f28d31/dqc_reference/reference_markers_gtdb.fasta -out GCF_001997185.1_ASM199718v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:09:34,351] [INFO] Task succeeded: Blastn
[2024-01-25 20:09:34,353] [INFO] Selected 11 target genomes.
[2024-01-25 20:09:34,353] [INFO] Target genome list was writen to GCF_001997185.1_ASM199718v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:09:34,392] [INFO] Task started: fastANI
[2024-01-25 20:09:34,393] [INFO] Running command: fastANI --query /var/lib/cwl/stg7a9f6ffb-da21-49ef-a12a-bd13fc7ed5fe/GCF_001997185.1_ASM199718v1_genomic.fna.gz --refList GCF_001997185.1_ASM199718v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001997185.1_ASM199718v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:09:49,619] [INFO] Task succeeded: fastANI
[2024-01-25 20:09:49,627] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:09:49,627] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_900186865.1	s__Stenotrophomonas maltophilia	99.9931	1578	1579	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	97.99	97.31	0.92	0.87	234	conclusive
GCF_006974125.1	s__Stenotrophomonas maltophilia_O	93.9616	1295	1579	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	98.85	98.84	0.92	0.90	5	-
GCF_003970865.1	s__Stenotrophomonas maltophilia_AR	93.7033	1252	1579	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013004645.1	s__Stenotrophomonas maltophilia_AM	93.3946	1293	1579	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	98.04	97.65	0.90	0.83	20	-
GCF_002799165.1	s__Stenotrophomonas maltophilia_Q	93.3595	1328	1579	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	97.69	95.30	0.93	0.83	9	-
GCF_013464915.1	s__Stenotrophomonas maltophilia_AT	93.2399	1256	1579	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	99.65	98.65	0.97	0.93	5	-
GCA_001431625.1	s__Stenotrophomonas geniculata	93.2068	1266	1579	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	97.51	96.26	0.87	0.77	45	-
GCF_004346925.1	s__Stenotrophomonas maltophilia_A	92.9556	1287	1579	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	97.29	95.44	0.89	0.84	41	-
GCF_002138415.1	s__Stenotrophomonas maltophilia_G	92.8673	1273	1579	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	95.93	95.59	0.89	0.87	14	-
GCF_000284595.1	s__Stenotrophomonas maltophilia_F	92.3186	1304	1579	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	98.76	98.38	0.92	0.88	60	-
GCF_006970445.1	s__Stenotrophomonas maltophilia_AU	92.2365	1268	1579	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:09:49,629] [INFO] GTDB search result was written to GCF_001997185.1_ASM199718v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:09:49,630] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:09:49,633] [INFO] DFAST_QC result json was written to GCF_001997185.1_ASM199718v1_genomic.fna/dqc_result.json
[2024-01-25 20:09:49,633] [INFO] DFAST_QC completed!
[2024-01-25 20:09:49,633] [INFO] Total running time: 0h1m44s